Re: Bug#834013: emboss, emboss-data: both packages ship /usr/share/man/man1/em_cons.1e.gz

Hi, this version was a source only upload. If I build on my local machine emboss-data does not contain any dir /usr/share/man. However, the binary package on the Debian mirror contains /usr/share/man/man1 with has two symlinks which are identical to those in the emboss package. I can not

Re: Bug#833288: would FTBFS now with cython 0.24.1 MACS2/IO/PeakIO.pyx:632:49: Cannot assign type 'float' to 'int'

Hi, I can confirm this bug. I've checked MACS2/IO/PeakIO.pyx and I think the typing of the function call should be fine - so probably the problem is somewhere else - but where? Any help would be welcome Andreas. On Tue, Aug 02, 2016 at 10:37:50AM -0400, Yaroslav Halchenko wrote: >

Re: Bug#832299: python-ruffus: FTBFS: sphinx.ext.mathjax: other math package is already loaded

On Mon, Jul 25, 2016 at 09:50:50PM +0200, Christian Seiler wrote: > If you really want your package to build _now_ for some > other reason, you could try to switch the dot format to png instead > of jpg (I would recommend png instead of jpg anyway for graphviz, > because jpg is more suitable for

Re: Bug#832299: python-ruffus: FTBFS: sphinx.ext.mathjax: other math package is already loaded

On Sun, Jul 24, 2016 at 12:43:02AM +0200, Chris Lamb wrote: > Running Sphinx v1.4.5 > making output directory... > WARNING: sphinx.ext.pngmath has been deprecated. Please use > sphinx.ext.imgmath instead. > > Extension error: > sphinx.ext.mathjax: other math package is already loaded

Please help upgrading eigensoft

Hi, I tried to upgrade eigensoft[1]. The build fails with: ... cc -Wl,-z,relro pca.o eigensrc/eigsubs.o eigx.o nicksrc/libnick.a -lgsl -lblas -lgfortran -lrt -lm -o pca eigx.o: In function `eigx_': /build/eigensoft-6.1.2+dfsg/src/eigx.c:100: undefined reference to `dspev_' eigx.o: In

Problems with opencl in pbuilder (Was: Bug#831235: libhmsbeagle: FTBFS: Tests failures)

Hi, it seems there is some opencl related problem when building libhmsbeagle in pbuilder (which worked before) On Thu, Jul 14, 2016 at 11:58:15AM +0200, Lucas Nussbaum wrote: > Source: libhmsbeagle > Version: 2.1.2+20151220-1 > Severity: serious > Tags: stretch sid > User:

Re: Bug#797280: Please help porting cufflinks to latest libboost

Hi Jakub, On Tue, Jul 12, 2016 at 01:10:44PM +0200, Jakub Wilk wrote: > > For some reason Eigen thinks that v.colwise().sum() cannot be treated as a > one-dimensional vector, which smells like a bug in Eigen. Changing the last > line to > > m = v.colwise().sum()(0, 0); > > seems to do

Please help porting cufflinks to latest libboost

Hi, in my last commit I tried to build cufflinks[1] against libboost 1.60 but failed. Since the failure does not seem to related to libboost I wonder whether somebody might be able to understand and fix this issue: ... In file included from /usr/include/eigen3/Eigen/Core:297:0,

d-shlibs: What package provides ld64-2-dev on ppc64 (and others) (Was: Next autoconf problem for today libdisorder)

Hi, On Tue, Jun 28, 2016 at 06:03:39PM +0200, Christian Seiler wrote: > > I agree that its not necessary to copy files around. However, I like > > d-shlibs to ensure that debian/control is properly designed. > > It does appear to not fully support all architectures though, if > you look at the

Re: How to specify a generic architecture to GCC (Was: SSE3 issue with iqtree when trying to enable i386)

Seiler wrote: > On 06/28/2016 11:01 AM, Andreas Tille wrote: > > I admit I can not answer the question asked by upstream. The package in > > question is iqtree[1] and they said that they have different > > computational kernels implemented to respect different hardware. &g

Re: Next autoconf problem for today libdisorder

On Tue, Jun 28, 2016 at 03:42:21PM +0200, Christian Seiler wrote: > > (Btw. you still didn't update debian/control in git. ;-)) Ahhh, thanks for noticing ... > Well, but the reason you get help here is so you can learn from > it. ;-) And you don't have to be an expert in the autotools (while I

How to specify a generic architecture to GCC (Was: SSE3 issue with iqtree when trying to enable i386)

Hi, I admit I can not answer the question asked by upstream. The package in question is iqtree[1] and they said that they have different computational kernels implemented to respect different hardware. Current Git[1] does not even build - may be due to some fine tuning of gcc options needed???

Re: Next autoconf problem for today libdisorder

Hi Christian, On Mon, Jun 27, 2016 at 11:57:12PM +0200, Christian Seiler wrote: > > Well, autoconf in and by itself doesn't support testing, automake does, > which fortunately you're also using. > > I've added a very trivial test from the way I understand how the program > you're using works,

Re: Next autoconf problem for today libdisorder

Hi Christian, On Mon, Jun 27, 2016 at 10:41:28PM +0200, Christian Seiler wrote: > On 06/27/2016 07:49 PM, Christian Seiler wrote: > > Other comments regarding the package: > > Oh btw. I just noticed that you don't install the manpage for > the library function in the -dev package (because

Re: Next autoconf problem for today libdisorder

aries that are using libdisorder. Thanks a lot for your great help Andreas. > [1] https://www.gnu.org/software/automake/manual/libtool.html#LT_005fINIT > Author: Andreas Tille <ti...@debian.org> > Last-Update: Wed, 22 Jun 2016 16:27:46 +0200 > Description: Add autoconf stuff t

Next autoconf problem for today libdisorder

Hi folks, ftpmaster spotted in two of my packages a code copy of libdisorder[1] which better should be packaged separately. Since I'd like to create dynamic and static library (upstream Makefile only creates static) I intended to add autoconf - but today I just proved that my skills are quite

Re: Help needed for autoreconf hmmer

Hi Jakub, On Mon, Jun 27, 2016 at 03:35:04PM +0200, Jakub Wilk wrote: > AUTOHEADER=true dh_autoreconf Thanks - works perfectly Andreas. -- http://fam-tille.de

Re: Help needed for autoreconf hmmer

;$EASEL_COPYRIGHT", [Define EASEL_COPYRIGHT]) > > > > Cheers, > > Neutron Soutmun > > > > On Mon, Jun 27, 2016 at 7:29 PM, Neutron Soutmun <neo.neut...@gmail.com> > > wrote: > >> Hi, > >> > >> On Mon, Jun 27, 20

Help needed for autoreconf hmmer

Hi, since ftpmaster rejected hmmer[1] due to a missing license statement for libdivsufsort code I verified that this library is packaged separately and tried to get rid of this code duplication at all. Thus I needed to autoreconfigure but failed: ... dh_autoreconf autoheader: warning:

Re: C++ help needed for libfastahack

Thanks for the always useful hints Andreas. On Thu, Jun 23, 2016 at 11:46:51AM +0200, Gert Wollny wrote: > Hello Andreas,  > > Am Donnerstag, den 23.06.2016, 11:24 +0200 schrieb Andreas Tille: > > Hi, > >  > > As I did yesterday successfully (thanks t

C++ help needed for libfastahack

Hi, I need to package libfastahack[1] as a pre-pre-dependency for some Debian Med package. The code comes with a manually crafted Makefile that simply creates an executable while the pre-depencency of my package[2] needs a devel package. As I did yesterday successfully (thanks to the help of

Re: [Debian-med-packaging] C++ help needed for libsmithwaterman

On Wed, Jun 22, 2016 at 03:04:06PM +0200, Gert Wollny wrote: > > I'll see what I can do to add these things, I expect to push this > > later today or tomorrow. > > Later as in: "I just did it" :)  Muchas gracias. Thanks for the very quick help Andreas. -- http://fam-tille.de

C++ help needed for libsmithwaterman

Hi, I need to package libsmithwaterman[1] as a pre-pre-dependency for some Debian Med package. The code comes with a manually crafted Makefile that simply creates an executable while the pre-depencency of my package[2] needs a devel package (tries to include one of the contained headers

Re: Problems building phast against clapack

Hi Barak, not sure whether you follow the discussion on debian-mentors[1] On Fri, Jun 03, 2016 at 03:47:16PM +0500, Andrey Rahmatullin wrote: > On Fri, Jun 03, 2016 at 11:20:09AM +0200, Andreas Tille wrote: > > In other words you mean this is a bug in libf2c2 package > Ye

Re: Problems building phast against clapack

On Fri, Jun 03, 2016 at 01:03:28PM +0500, Andrey Rahmatullin wrote: > On Fri, Jun 03, 2016 at 09:59:00AM +0200, Andreas Tille wrote: > > ../munge-help.sh consEntropy.help_src > consEntropy.help > > gcc -O3 -Wall -I/build/phast-1.4/src/util/../../include > > -DPHAST_VERSI

Problems building phast against clapack

Hi, I recently have createt a package from clapack to build phast[1]. Unfortunately the build fails for reasons I do not understand. I expect that something might be wrong with either f2c or clapack packaging but I'm not sure. Anybody might be able to make some sense out of: ...

Re: Help for backport of seer wanted (may be libhdf5 problem?)

/debian/ jessie/main amd64 Packages installed while a build in a Jessie+backports chroot fails. Do you think the solution is that simple as backporting armadillo 6.700.6+dfsg-1 ? Kind regards Andreas. > Il Lunedì 30 Maggio 2016 11:10, Andreas Tille <andr...@an3as.eu> ha scri

Help for backport of seer wanted (may be libhdf5 problem?)

Hi, I intend to backport seer[1] but I was running into a build issue: ... g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -fPIE -pie

Re: Trying to disable error=format-security for clapack

Hi Gert, On Thu, May 26, 2016 at 04:27:25PM +0200, Gert Wollny wrote: > ... > Removing the file INCLUDE/f2c.h solves the problem, because then the > ... This tip saved my evening yesterday - thanks a lot. The only remaining issue is now E: libclapack3: binary-or-shlib-defines-rpath

Re: Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing

On Fri, May 27, 2016 at 10:05:03AM +0200, Jakub Wilk wrote: > * Andreas Tille <andr...@an3as.eu>, 2016-05-27, 09:27: > >>/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/Scrt1.o: In > >>function `_start': > >>(.text+0x20): undefined reference to `main

Re: [Help] Re: Bug#825461: staden: FTBFS in testing

Hi Gianfranco, On Fri, May 27, 2016 at 07:53:45AM +, Gianfranco Costamagna wrote: > Hi, some quick googling found some possible solutions > https://www.google.it/search?client=ubuntu=fs=%22Scrt1.o%3A+In+function+`_start%27%3A%22=utf-8=utf-8_rd=cr=5ftHV7_JI8fA8geO-LmABQ > > I remember having

[Help] Re: Bug#825461: staden: FTBFS in testing

Hi, On Fri, May 27, 2016 at 02:29:28AM +0200, Santiago Vila wrote: > -- > capture.o: In function `tcl_capture': > /<>/staden-2.0.0+b10/tk_utils/capture.c:31: warning: the use of > `tmpnam' is dangerous, better use `mkstemp' I've

Re: [Debian-med-packaging] Trying to disable error=format-security for clapack

Hi Gianfranco, On Sun, May 22, 2016 at 06:48:36AM +, Gianfranco Costamagna wrote: > ... > I would say: remove the add_subdirectory (line 21) > and then: > 1) create a "FindF2C.cmake" file and use it as helper > (that would be the best and upstreamable choice > you can find some examples in

Re: [Debian-med-packaging] Trying to disable error=format-security for clapack

Sorry for replying to my own mail. I just noticed that the Debian packaged libf2c really has no symbol i_len_trim. Will check what version is packaged and how this can be fixed. On Mon, May 23, 2016 at 12:08:08PM +0200, Andreas Tille wrote: > Hi Gianfranco, > > your very helpful hin

Re: [Debian-med-packaging] Trying to disable error=format-security for clapack

Hi Gianfranco, your very helpful hints helped me to get some steps forward. However, its not finally done. On Sun, May 22, 2016 at 06:48:36AM +, Gianfranco Costamagna wrote: > >Another question is how I could link against the Debian packaged f2c > >rather than building the one that comes

Missing latest version of libgtk-3-common in unstable?

Hi, is anybody else observing this: $ LC_ALL=C apt-cache policy libgtk-3-common libgtk-3-0 libgtk-3-common: Installed: 3.20.4-1 Candidate: 3.20.4-1 Version table: *** 3.20.4-1 501 501 http://httpredir.debian.org/debian testing/main amd64 Packages 100 /var/lib/dpkg/status

Re: [Debian-med-packaging] Trying to disable error=format-security for clapack

Hi again, after the build issues in clapack[1] were solved and I was even able to create shared libraries I wonder how I can properly set a sensible SONAME. I tried to do this via SET_TARGET_PROPERTIES but failed. Another question is how I could link against the Debian packaged f2c rather than

Re: Trying to disable error=format-security for clapack

Hi Danny, On Mon, May 16, 2016 at 04:30:23PM +0200, Danny Edel wrote: > Sorry for replying to my own email, but after compiling, the test suite > crashed on the xeigtstz_* with Segmentation Fault errors. No need to sorry, > I debugged this a little bit and the reason was these tests use a lot

Trying to disable error=format-security for clapack

Hi, as a precondition for some package for Debian Med I intend to package clapack[1]. Despite the discussion on Debian Science about the relation of clapack and lapacke[2] I decided that it is less effort to have clapack in addition since upstream of phast[3] (my final target) does not intend to

Re: Bug#818505: sortmerna FTBFS on !x86

On Sun, Mar 27, 2016 at 08:15:27PM +0200, Adam Borowski wrote: > > It might be also good to make a "sse2-support" package as mentioned in the > thread Gert linked to to reduce duplication of such detection logic. Please > say so if you think this is a good idea. Saying "so". :-) Yes, having

Doxygen help needed (Was: FTBFS: error while building documentation)

ything works as expected, without error. > Maybe there was an error in 1.6.5, but so far it seems to have been fixed. > > Regards, > > David. > > 2016-04-28 16:45 GMT+02:00 Andreas Tille <andr...@an3as.eu>: > > > Hi David, > > > > there is a

Re: How to avoid version restrictions for JS libraries (Was: Bug#820879: r-cran-shiny: uninstallable in sid: Depends: libjs-jquery (< 1.11.3+dfsg.0~) but 1.12.3-1 is to be installed)

Hi Raphael, On Thu, Apr 14, 2016 at 12:00:26PM +0200, Raphael Hertzog wrote: > > So I did have a look and the problem is that your package doesn't contain any > usr/lib/R/site-library/shiny/www/shared/jqueryui/images to replace > with some real files. > > I added this to check it: >

Re: How to avoid version restrictions for JS libraries (Was: Bug#820879: r-cran-shiny: uninstallable in sid: Depends: libjs-jquery (< 1.11.3+dfsg.0~) but 1.12.3-1 is to be installed)

On Thu, Apr 14, 2016 at 10:02:43AM +0200, Raphael Hertzog wrote: > On Wed, 13 Apr 2016, Andreas Tille wrote: > > The thing is I used "replace" in the first place instead of embed but > > it resulted in > > > > dh_linktree > > dpkg-query: error: --

Re: Bug#820879: How to avoid version restrictions for JS libraries (Was: Bug#820879: r-cran-shiny: uninstallable in sid: Depends: libjs-jquery (< 1.11.3+dfsg.0~) but 1.12.3-1 is to be installed)

On Wed, Apr 13, 2016 at 09:37:00PM +0200, Andreas Tille wrote: > On Wed, Apr 13, 2016 at 03:38:16PM +0200, Raphael Hertzog wrote: > > On Wed, 13 Apr 2016, Andreas Tille wrote: > > > Could you advise for the proper option to get a less strict dependency? > > > > Ple

Re: How to avoid version restrictions for JS libraries (Was: Bug#820879: r-cran-shiny: uninstallable in sid: Depends: libjs-jquery (< 1.11.3+dfsg.0~) but 1.12.3-1 is to be installed)

On Wed, Apr 13, 2016 at 03:38:16PM +0200, Raphael Hertzog wrote: > On Wed, 13 Apr 2016, Andreas Tille wrote: > > Could you advise for the proper option to get a less strict dependency? > > Please read its manual page, it's all documented: > > | The "replace" acti

Re: How to avoid version restrictions for JS libraries (Was: Bug#820879: r-cran-shiny: uninstallable in sid: Depends: libjs-jquery (< 1.11.3+dfsg.0~) but 1.12.3-1 is to be installed)

Hi Raphael, On Wed, Apr 13, 2016 at 02:41:52PM +0200, Raphael Hertzog wrote: > > It really depends... you're trading one problem for another. In general, > it's best if you can just rely on the packaged javascript without having > to replace any embedded copy. > > But if you have to replace an

Re: How to avoid version restrictions for JS libraries (Was: Bug#820879: r-cran-shiny: uninstallable in sid: Depends: libjs-jquery (< 1.11.3+dfsg.0~) but 1.12.3-1 is to be installed)

Hi James, On Wed, Apr 13, 2016 at 12:28:58PM +0100, James Cowgill wrote: > On Wed, 2016-04-13 at 13:13 +0200, Andreas Tille wrote: > > via this bug I learned (the hard way) that a > > > >    Depends: ${js:Depends} > > > > will be resolved into > > > &g

How to avoid version restrictions for JS libraries (Was: Bug#820879: r-cran-shiny: uninstallable in sid: Depends: libjs-jquery (< 1.11.3+dfsg.0~) but 1.12.3-1 is to be installed)

Hi, via this bug I learned (the hard way) that a Depends: ${js:Depends} will be resolved into libjs-jquery (<< 1.11.3+dfsg.0~), libjs-jquery (>= 1.11.3+dfsg) (for instance) in the final package. I have no reason to assume that the actual version that was available at package build time

Re: Any reason to keep libsdsl in experimental (Was: Please help creating shared *and* static library with cmake)

Hi Tomasz, On Sat, Apr 09, 2016 at 04:47:35PM +0200, Tomasz Buchert wrote: > > the only reason is that it doesn't build on most architectures. The > upstream devel version build, I think, on other archs, but it hasn't > been released yet. I've asked the upstream author to release a new >

Any reason to keep libsdsl in experimental (Was: Please help creating shared *and* static library with cmake)

On Fri, Apr 08, 2016 at 06:16:51PM +0100, Sascha Steinbiss wrote: > For the record, I seem to remember there is already a libsdsl package in > experimental: > https://packages.qa.debian.org/libs/libsdsl.html Ahhh, very helpful hint!! Tomasz, is there any reason to have this package in

Re: Please help creating shared *and* static library with cmake

On Fri, Apr 08, 2016 at 05:53:48PM +0200, Ole Streicher wrote: > Andreas Tille <andr...@an3as.eu> writes: > > I need to package libsdsl[1] as some precondition for a Debian Med > > package. The default cmake build only creates a static library and I > > found a patch

Re: Please help creating shared *and* static library with cmake

On Fri, Apr 08, 2016 at 06:13:13PM +0200, Joachim Reichel wrote: > in the "cgal" package I basically build the package twice: > > override_dh_auto_configure-arch: > mkdir -p static > cd static && cmake .. -DBUILD_SHARED_LIBS=FALSE > mkdir -p shared > cd shared && cmake ..

Please help creating shared *and* static library with cmake

Hi, I need to package libsdsl[1] as some precondition for a Debian Med package. The default cmake build only creates a static library and I found a patch to create a shared library. But since library packages should include both I wonder how to get both shared and static library without doing

Re: Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

Hi Jakub, On Tue, Mar 29, 2016 at 10:01:51PM +0200, Jakub Wilk wrote: > > https://github.com/johnlees/seer links to: > http://www.cs.unc.edu/Research/compgeom/gzstream/ > > AFAICT, this is not packaged for Debian. (Although we have multiple embedded > code copies[0]. Yay...) See #819532. Kind

Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

Hi, I'm trying to package seer[1] for the Debian Med team. Upstream provides a simple Makefile which is probably the cause why the libraries for linking are not found properly so it ends up in ... g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11

Bug#819391: Please use Git repository layout as described in Debian Science policy

Hi Thomas, I had a look into the repository of toulbar2[1] since you asked for sponsering of the package. I noticed that it does not follow the repository layout as specified in the Debian Science policy[2] and also the control file diverges from Debian Science policy (Maintainer should be the

Re: Bug#818505: sortmerna FTBFS on !x86

Hi Jurica, On Thu, Mar 17, 2016 at 05:04:21PM +, Jurica Stanojkovic wrote: > Package sortmerna FTBFS on archs not in x86 group (amd64, i386, x32, etc. ) > with following error: > gcc: error: unrecognized command line option '-msse2' > > build logs: >

Bug#818623: STatus of r-cran-uuid?

d, Mar 23, 2016 at 10:57:45AM +0100, Andreas Tille wrote: > > > it seems this package was in NEW queue but it is not any more and I also > > > can't find it in the package pool. Could you please give some status > > > update? > > > > it has been accepte

Bug#818623: STatus of r-cran-uuid?

Hi, it seems this package was in NEW queue but it is not any more and I also can't find it in the package pool. Could you please give some status update? I'd suggest to move the package to Debian Science Git and I'd volunteer to do so but it would be good to know if and why it was rejected.

Bug#818622: ITP: r-cran-r6 -- R classes with reference semantics

Hi Gordon, I realised to late that you also ITPed r-cran-r6 and issued another ITP for this package. I noticed as well that you opened another "versioned" ITP as bug #818622 which is a bit unusual, thought. I intended to package this as well for the Debian Med team. Since your ITP was first I

Re: Help with new version of iqtree needed

Hi James, thanks for the fast response: On Thu, Mar 10, 2016 at 01:49:23PM +, James Cowgill wrote: > On Thu, 2016-03-10 at 14:39 +0100, Andreas Tille wrote: > > Hi, > > > > I#m facing a C++ problem with the new version of iqtree.  If I build the > > cu

Help with new version of iqtree needed

Hi, I#m facing a C++ problem with the new version of iqtree. If I build the current state in Git[1] I get: ... [ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-1.4.0+dfsg/obj-x86_64-linux-gnu/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -D__SSE3

[Help] Re: pandas FTBFS on BE platforms due to a bunch of tests failures

Hi, while pandas builds on intel it fails on several other architectures as reported in #814795. This has been reported upstream[1] who does not seem to be really interested in solving the issue. Any help from porters would be really welcome. Thanks a lot Andreas. [1]

Bug#814727: Latex not found

Hi, when trying to build the package I get ... warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. sh: 1: latex: not found sh: 1: dvips: not found ... I

Problems using OpenCL in pbuilder (Was: OpenCL GPU usage on autobuilders)

wonder what exactly I need to do to let the test below pass and enable the detection of a smart enough GPU in pbuilder. Thanks for any help Andreas. On Sun, Jan 31, 2016 at 08:27:46AM +0100, Andreas Tille wrote: > Hi, > > I just realised that the issue also happens on my loca

Re: OpenCL GPU usage on autobuilders (Was: Bug#813262: python-biopython: FTBFS: ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa')

Hi, I just realised that the issue also happens on my local machine - so the assumption that only autobuilders are affected is wrong. I think I just need to fix the dependencies for libhmsbeagle-dev. Sorry for the noise Andreas. On Sun, Jan 31, 2016 at 07:56:31AM +0100, Andreas Tille wrote

OpenCL GPU usage on autobuilders (Was: Bug#813262: python-biopython: FTBFS: ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa')

Hi, On Sat, Jan 30, 2016 at 11:51:26PM +0100, Chris Lamb wrote: > Source: python-biopython > Version: 1.66+dfsg-1 > Severity: serious > Justification: fails to build from source > ... > ApplicationError: Non-zero return code 255 from 'phyml -i > Phylip/interlaced2.phy -d aa', message

Re: Bug#812681: [help] Bug#812681: mira: FTBFS with flex >= 2.6]

Hi Jakub, On Tue, Jan 26, 2016 at 05:12:26PM +0100, Jakub Wilk wrote: > * Andreas Tille <andr...@an3as.eu>, 2016-01-25, 22:06: > >sorry, I have no idea about fley and need help to fix this problem. > > I think it's a bit premature to ask debian-mentors for help when your

[help] Bug#812681: mira: FTBFS with flex >= 2.6]

Hi, sorry, I have no idea about fley and need help to fix this problem. Any hint would be welcome. Kind regards Andreas. - Forwarded message from Michael Tautschnig - During a rebuild of all Debian packages in a clean sid chroot (using cowbuilder and

Re: Failed to stop defining RPATH in libncl

On Mon, Jan 04, 2016 at 05:19:42PM +, Wookey wrote: > +++ Andreas Tille [2016-01-04 16:19 +0100]: > > On Mon, Jan 04, 2016 at 03:07:40PM +, Wookey wrote: > > > > E: ncl-tools: binary-or-shlib-defines-rpath usr/bin/NCLconverter > > > > /usr/lib/x86_64-l

Failed to stop defining RPATH in libncl

Hi, I'm trying to package libncl[1] but I failed to fight the following lintian error: E: ncl-tools: binary-or-shlib-defines-rpath usr/bin/NCLconverter /usr/lib/x86_64-linux-gnu/ncl N: N:The binary or shared library sets RPATH. This overrides the normal N:library search path, possibly

Re: Failed to stop defining RPATH in libncl

Hi Gianfranco, thanks for your attempt to help. On Mon, Jan 04, 2016 at 01:03:51PM +, Gianfranco Costamagna wrote: > I think there is no way for a binary to pick something not in usr/lib or > usr/lib/{triplet} > > unless you want to add a new ld.so.conf.d file > cat /etc/ld.so.conf.d/* >

Re: Failed to stop defining RPATH in libncl

On Mon, Jan 04, 2016 at 03:07:40PM +, Wookey wrote: > > E: ncl-tools: binary-or-shlib-defines-rpath usr/bin/NCLconverter > > /usr/lib/x86_64-linux-gnu/ncl > > N: > > N:The binary or shared library sets RPATH. This overrides the normal > > N:library search path, possibly interfering

Please help (Was: Bug#808537: jellyfish: FTBFS: error: 'template class std::auto_ptr' is deprecated [-Werror=deprecated-declarations])

Hi, I was hoping that Gert could provide any hint how he fixed #778005 but he seems to be offline. Any hint how to deal with his? Kind regards Andreas. - Forwarded message from Andreas Tille <andr...@an3as.eu> - Date: Sun, 20 Dec 2015 17:46:54 +0100 From: Andreas Tille

Re: Please help (Was: Bug#808537: jellyfish: FTBFS: error: 'template class std::auto_ptr' is deprecated [-Werror=deprecated-declarations])

ou able to respond without keyboard? ;-) Very cool - thanks a lot! > - Forwarded message from Andreas Tille <andr...@an3as.eu> - > > Cc: Gert Wollny <gw.foss...@gmail.com> > > Subject: Re: Bug#808537: jellyfish: FTBFS: error: 'template > > class std::auto_

cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.

Hi, I'm trying to fix libsbml bugs and while doing so upgrade to the latest upstream version. Since the original tarball needs to be stripped I moved the packaging from SVN to Git[1] (so please do not try debcheckout which does not lead to the latest packaging status). Unfortunately my attempt

Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.

Hi Kevin, On Thu, Dec 17, 2015 at 10:44:40PM +1100, Kevin Murray wrote: > > I have pushed a possible fix to the branch 'daube/possible-cmake-fix'. I am > not > sure of the overall effects, the build is taking ages on my laptop, but it > seems > to have fixed the immediate error. Thanks a lot

Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.

lution to the problem. Comments? Kind regards Andreas. > -------- > Gio 17/12/15, Andreas Tille <andr...@fam-tille.de> ha scritto: > > Oggetto: Re: cmake issue in libsbml: Cannot generate java documentation, > please specify the

Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.

Hi Jakub, On Thu, Dec 17, 2015 at 11:34:53PM +0100, Jakub Wilk wrote: > * Andreas Tille <andr...@an3as.eu>, 2015-12-17, 19:11: > >override_dh_auto_build: > >+ if mount | grep "^proc " ; then echo "proc mounted - fine"; else > >mount p

Re: DNS fails in pbuilder

On Fri, Dec 11, 2015 at 03:10:23PM +0100, Andreas Tille wrote: > On Fri, Dec 11, 2015 at 01:26:31PM +, Mattia Rizzolo wrote: > > > I tried pbuilder 0.221.1 from testing and 0.221.3 from unstable. > > > > Should be fixed by 0.221.2, are you sure it's still broken, be

Lintian leaves me with error when Build-Depending from qt5-default :-( (Was: C++ / Qt help for Ugene needed)

Hi, On Thu, Dec 10, 2015 at 08:28:36PM +0100, Gert Wollny wrote: > On Thu, 2015-12-10 at 14:07 +0100, Andreas Tille wrote: > > I'd be really delighted if you get this built! > > It should build now, at least here it just did in an freshly updated > pbuilder environment.

DNS fails in pbuilder

Hi, since one week I'm observing that when moving to different networks pbuilder fails to resolve any host names. I was able to cure it by copying my local /etc/resolv.conf to /var/cache/pbuilder/base.cow/etc/resolv.conf but in principle I do not even understand how this could have worked before

Re: DNS fails in pbuilder

On Fri, Dec 11, 2015 at 01:26:31PM +, Mattia Rizzolo wrote: > > I tried pbuilder 0.221.1 from testing and 0.221.3 from unstable. > > Should be fixed by 0.221.2, are you sure it's still broken, because > several people confirmed me it's fixed... I confirm that the problem persits in 0.221.3

C++ / Qt help for Ugene needed

Hi folks, I tried to upgrade ugene to the new upstream package. When doing so I moved the packaging to Git[1]. Unfortunately I'm running into a build error: ... g++ -c -m64 -pipe -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O2 -D_REENTRANT -Wall -W

Bug#805521: Fwd: Bug#805521: RFS: normaliz/3.0.0+ds-2 [FTBFS fix release]

Hi Jerome, I get E: libnormaliz0: postinst-must-call-ldconfig usr/lib/x86_64-linux-gnu/libnormaliz.so.3.0.0 N: N:The package installs shared libraries in a directory controlled by the N:dynamic library loader. Therefore, the package must call "ldconfig" in N:its postinst script. N:

Re: Bug#805521: Fwd: Bug#805521: RFS: normaliz/3.0.0+ds-2 [FTBFS fix release]

Ahh, sorry. I was not building on my usual build machine ... On Thu, Nov 19, 2015 at 05:57:07PM +0100, Jerome BENOIT wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hello Forum: > > On 19/11/15 12:48, Jakub Wilk wrote: > > * Andreas Tille <andr...@a

Bug#803674: latex not found in opengm

Hi Ghislain, in the opengm build log I've found: ... /usr/bin/doxygen /build/opengm-2.3.6/obj-x86_64-linux-gnu/Doxyfile Warning: Tag `SYMBOL_CACHE_SIZE' at line 310 of file `/build/opengm-2.3.6/obj-x86_64-linux-gnu/Doxyfile' has become obsolete. To avoid this warning please remove this

Bug#803674: latex not found in opengm

Hi Ghislain, On Mon, Nov 02, 2015 at 08:29:42AM +, Ghislain Vaillant wrote: > > > >Did you checked whether the documentation is properly built? > > Yes, although the -doc package only contains the HTML documentation. I > checked it and it runs fine. I can add the pdf build if it is a

Re: Help needed: Bug#802354: python-matplotlib-venn: FTBFS: AttributeError: can't set attribute

On Fri, Oct 23, 2015 at 01:43:19AM +0200, Tomasz Buchert wrote: > this is due to [1]. It seems that 'test_args' is a property. > I didn't dig very deep, but the attached patch seems to fix this. Thanks a lot - that worked Andreas. -- http://fam-tille.de

Re: Help needed to build libhmsbeagle using OpenCL

Hi, I have a totally different question about OpenCL: Assume I have successfully built it locally. When checking the availability of libhmsbeagle features beast-mcmc (which uses libhmsbeagle) provides a check which in my case looks like: $ java -jar /usr/share/beast-mcmc/beast.jar -beagle

Help needed: Bug#802354: python-matplotlib-venn: FTBFS: AttributeError: can't set attribute

Hi, I have no idea why this package now fails to build but was building before. No helpful response from debian-python list so far. I opened an issue at Github but upstream needs time to reproduce and I hope that this might be a know issue to others here on this list. Any hint would be welcome

Re: Help needed to build libhmsbeagle using OpenCL

Hi Ghislain, On Wed, Oct 21, 2015 at 02:33:37PM +0100, Ghislain Vaillant wrote: > Hi Andreas, my answer inline below sure. ;-) > >advantages when using OpenCL. I personally do not have any experience > >with OpenCL and simply added > > > > libpoclu-dev, > > ocl-icd-opencl-dev > > > >

Re: Help needed to build libhmsbeagle using OpenCL

On Wed, Oct 21, 2015 at 03:38:12PM +0100, Ghislain Vaillant wrote: > ># cat tmp/buildd/libhmsbeagle-2.1.2+20150609/examples/tinytest/tinytest.log > > > >OpenCL error: CL_DEVICE_NOT_FOUND from file , line > >118. > >FAIL tinytest (exit status: 255) > > The error comes from their GPU interface

Re: Bug#725434: Problems with gbp when $TMP != /tmp

On Tue, Oct 20, 2015 at 05:16:06PM +, Mattia Rizzolo wrote: > > pbuilder: > > Installed: 0.215+nmu4~bpo8+1 > > Candidate: 0.215+nmu4~bpo8+1 > > well, please `apt update` :) > I uploaed 0.219~bpo8+1 2 days ago ^^ Installed - but I need the `chmod 777` part with this one ... Kind regards

Help needed to build libhmsbeagle using OpenCL

Hi, I've got the hint that libhmsbeagle only expresses its real performance advantages when using OpenCL. I personally do not have any experience with OpenCL and simply added libpoclu-dev, ocl-icd-opencl-dev as Build-Depends as well as using the configure option

Re: Bug#725434: Problems with gbp when $TMP != /tmp

Hi Mattia, On Tue, Oct 20, 2015 at 04:18:55PM +, Mattia Rizzolo wrote: > On Tue, Oct 20, 2015 at 03:07:55PM +0200, Andreas Tille wrote: > > I'm obviously beaten by bug #725434 when trying to use gbp on a stable > > box with libpam-tmpdir. I followed the workaround and added a

Problems with gbp when $TMP != /tmp

Hi, I'm obviously beaten by bug #725434 when trying to use gbp on a stable box with libpam-tmpdir. I followed the workaround and added a hook script: $ cat .pbuilder/D10tmp #!/bin/bash # Work around #725434 # example file to be used with --hookdir # #create $TMP and $TMPDIR echo

Re: Java problem when upgrading pixelmed

On Tue, Oct 06, 2015 at 10:36:56PM +0200, Emmanuel Bourg wrote: > Le 06/10/2015 22:28, Andreas Tille a écrit : > > > export JAVAVERSIONTARGETJARFILE=/usr/lib/jvm/default-java/jre/lib/rt.jar; > > javac -O -target 1.7 -source 1.7 -bootclasspath ${JAVAVERSIONTARGETJARFILE} &

Re: Java problem when upgrading pixelmed

Hi, On Thu, Oct 08, 2015 at 01:40:58PM +0200, Bas Couwenberg wrote: > On 2015-10-08 13:28, Emmanuel Bourg wrote: > >It looks like you need the new standard Java API for JSON processing > >(JSR 353) [1], we haven't packaged it yet, but josm has a local copy (if > >you search for 'package

Java problem when upgrading pixelmed

Hi, I tried to upgrade pixelmed[1] to the latest version (20150917 as per trunk in SVN) but the build failed with export JAVAVERSIONTARGETJARFILE=/usr/lib/jvm/default-java/jre/lib/rt.jar; javac -O -target 1.7 -source 1.7 -bootclasspath ${JAVAVERSIONTARGETJARFILE} -encoding "UTF8" -Xlint:

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